Processing of the Escherichi coli leuX tRNA transcript, encoding tRNALeu5, requires either the 3′→5′ exoribonuclease polynucleotide phosphorylase or RNase P to remove the Rho-independent transcription terminator

Nucleic Acids Research

Volumn 38, Issue 2, 2009, Pages 597-607

  Mohanty, Bijoy K ^a   Kushner, Sidney R ^a  

^a University of Georgia ^*  (United States)

Author keywords

[No Author keywords available]

Indexed keywords

EXORIBONUCLEASE; LEUCINE; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; PROTEIN RHIB; RHO FACTOR; RIBONUCLEASE; RIBONUCLEASE E; RIBONUCLEASE G; RIBONUCLEASE P; RIBONUCLEASE Z; RNA HELICASE; TRANSFER RNA; UNCLASSIFIED DRUG; ACID ANHYDRIDE HYDROLASE; DEAD BOX PROTEIN; ESCHERICHIA COLI PROTEIN; EXORIBONUCLEASE II; EXORIBONUCLEASE T; LEUCINE TRANSFER RNA; RHLB PROTEIN, E COLI; RHO PROTEIN, E COLI; RIBONUCLEASE P, E COLI; RPPH PROTEIN, E COLI;

3' UNTRANSLATED REGION; 5' UNTRANSLATED REGION; ARTICLE; CONTROLLED STUDY; DOWNSTREAM PROCESSING; ESCHERICHIA COLI; IN VIVO STUDY; NONHUMAN; PRIORITY JOURNAL; PROTEIN SECONDARY STRUCTURE; RNA DEGRADATION; RNA PROCESSING; RNA TRANSCRIPTION; TRANSCRIPTION TERMINATION; CHEMISTRY; ENZYMOLOGY; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; POLYADENYLATION;

ESCHERICHIA COLI;

5' UNTRANSLATED REGIONS; ACID ANHYDRIDE HYDROLASES; DEAD-BOX RNA HELICASES; ENDORIBONUCLEASES; ESCHERICHIA COLI; ESCHERICHIA COLI PROTEINS; EXORIBONUCLEASES; GENE EXPRESSION REGULATION, BACTERIAL; POLYADENYLATION; POLYRIBONUCLEOTIDE NUCLEOTIDYLTRANSFERASE; RIBONUCLEASE P; RNA 3' END PROCESSING; RNA, TRANSFER, LEU;

EID: 77449094737     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkp997     Document Type: Article

References (36)

1. Altman, S., Kirsebom, L. and Talbot, S. (1995) Recent studies of RNase P. In Soll, D. and RajBhandary. (eds), tRNA: Structure and Function. American Society for Microbiology Press, Washington, DC, pp. 67-78.
2. Morl, M. and Marchfelder, A. (2001) The final cut. The importance of tRNA 3′-processing. EMBO Rep., 2, 17-20.
3. Li, Z. and Deutscher, M.P. (2002) RNase E plays an essential role in the maturation of Escherichia coli tRNA precursors. RNA, 8, 97-109.
4. Ow, M.C. and Kushner, S.R. (2002) Initiation of tRNA maturation by RNase E is essential for cell viability in Escherichia coli. Genes Dev., 16, 1102-1115.
5. Mohanty, B.K. and Kushner, S.R. (2008) Rho-independent transcription terminators inhibit RNase P processing of the secG leuU and metT tRNA polycistronic transcripts in Escherichia coli. Nucleic Acids Res., 36, 364-375.
6. Mohanty, B.K. and Kushner, S.R. (2007) Ribonuclease P processes polycistronic tRNA transcripts in Escherichia coli independent of ribonuclease E. Nucleic Acids Res., 35, 7614-7625.
7. Deutscher, M.P. (2006) Degradation of RNA in bacteria: comparison of mRNA and stable RNA. Nucleic Acids Res., 34, 659-666.
8. Li, Z. and Deutscher, M.P. (1996) Maturation pathways for E. coli tRNA precursors: a random multienzyme process in vivo. Cell, 86, 503-512.
9. Spickler, C. and Mackie, G.A. (2000) Action of RNase II and polynucleotide phosphorylase against RNAs containing stem-loops of defined structure. J. Bacteriol., 182, 2422-2427.
10. Schedl, P. and Primakoff, P. (1973) Mutants of Escherichia coli thermosensitive for the synthesis of transfer RNA. Proc. Natl Acad. Sci. USA, 70, 2091-2095.
11. Arraiano, C.M., Yancey, S.D. and Kushner, S.R. (1988) Stabilization of discrete mRNA breakdown products in ams pnp rnb multiple mutants of Escherichia coli K-12. J. Bacteriol., 170, 4625-4633.
12. Ono, M. and Kuwano, M. (1979) A conditional lethal mutation in an Escherichia coli strain with a longer chemical lifetime of mRNA. J. Mol. Biol., 129, 343-357.
13. Mohanty, B.K. and Kushner, S.R. (2003) Genomic analysis in Escherichia coli demonstrates differential roles for polynucleotide phosphorylase and RNase II in mRNA abundance and decay. Mol. Microbiol., 50, 645-658.
14. Piedade, J., Zilhao, R. and Arraiano, C.M. (1995) Construction and characterization of an absolute deletion of Escherichia coli ribonuclease II. FEMS Microbiol. Lett., 127, 187-193.
15. Donovan, W.P. and Kushner, S.R. (1986) Polynucleotide phosphorylase and ribonuclease II are required for cell viability and mRNA turnover in Escherichia coli K-12. Proc. Natl Acad. Sci. USA, 83, 120-124.
16. Khemici, V., Toesca, I., Poljak, L., Vanzo, N.F. and Carpousis, A.J. (2004) The RNase E of Escherichia coli has at least two binding sites for DEAD-box RNA helicases: functional replacement of RhlB by RhlE. Mol. Microbiol., 54, 1422-1430.
17. Mohanty, B.K., Giladi, H., Maples, V.F. and Kushner, S.R. (2008) Analysis of RNA decay, processing. amd polyadenylation in Eschericha coli and other prokaryotes. In Arraiano, C.M. and Maquat, L. (eds), Methods Enzymol, Vol. 447. Academic Press, pp. 3-29.
18. Perwez, T. and Kushner, S.R. (2006) RNase Z in Escherichia coli plays a significant role in mRNA decay. Mol. Microbiol., 60, 723-737.
19. Nomura, T., Fujita, N. and Ishihama, A. (1987) Expression of the leuX gene in Escherichia coli: Regulation at transcription and tRNA processing steps. J. Mol. Biol., 197, 659-670.
20. Deana, A., Celesnik, H. and Belasco, J.G. (2008) The bacterial enzyme RppH triggers messenger RNA degradation by 5′ pyrophosphate removal. Nature, 451, 355-358.
21. Tock, M.R., Walsh, A.P., Carroll, G. and McDowall, K.J. (2000) The CafA protein required for the 5′-maturation of 16S rRNA is a 5′-end-dependent ribonuclease that has context-dependent broad sequence specificity. J. Biol. Chem., 275, 8726-8732.
22. Mackie, G.A. (1998) Ribonuclease E is a 5′-end-dependent endonuclease. Nature, 395, 720-723.
23. Mackie, G.A. (2000) Stabilization of circular rpsT mRNA demonstrates the 5′-end dependence of RNase E action in vivo. J. Biol. Chem., 275, 25069-25072.
24. Mathy, N., Benard, L., Pellegrini, O., Daou, R., Wen, T. and Condon, C. (2007) 5′-to-3′ exoribonuclease activity in bacteria: role of RNase J1 in rRNA maturation and 5( stability of mRNA. Cell, 129, 681-692.
25. Vincent, H.A. and Deutscher, M.P. (2006) Substrate recognition and catalysis by the exoribonuclease RNase R. J. Biol. Chem., 281, 29769-29775.
26. Zuo, Y. and Deutscher, M.P. (2002) The physiological role of RNase T can be explained by its unusual substrate specificity. J. Biol. Chem., 277, 29654-29661.
27. Liou, G-G., Chang, H.-Y., Lin, C.S. and Lin-Chao, S. (2002) DEAD box RhlB RNA helicase physically associates with exoribonuclease PNPase to degrade double-stranded RNA independent of the degradosome-assembling region of RNase E. J. Biol. Chem., 277, 41157-41162.
28. Coburn, G.A., Miao, X., Briant, D.J. and Mackie, G.A. (1999) Reconstitution of a minimal RNA degradosome demonstrates functional coordination between a 3′ exonuclease and a DEAD-box RNA helicase. Genes Dev., 13, 2594-2603.
29. Blum, E., Carpousis, A.J. and Higgins, C.F. (1999) Polyadenylation promotes degradation of 3′-structured RNA by the Escherichia coli mRNA degradosome in vitro. J. Biol. Chem., 274, 4009-4016.
30. Nomura, T. and Ishihama, A. (1988) A novel function of RNase P from Escherichia coli: processing of a suppressor tRNA precursor. EMBO J., 7, 3539-3545.
31. Gultyaev, A.P., van Batenburg, F.H.D. and Pleij, C.W.A. (1995) The computer simulation of RNA folding pathways using a genetic algorithm. J. Mol. Biol., 250, 37-51.
32. Coburn, G.A. and Mackie, G.A. (1998) Reconstitution of the degradation of the mRNA for ribosomal protein S20 with purified enzymes. J. Mol. Biol., 279, 1061-1074.
33. Zilhao, R., Cairrao, R., Régnier, P. and Arraiano, C.M. (1996) PNPase modulates RNase II expression in Escherichia coli: Implications for mRNA decay and cell metabolism. Mol. Microbiol., 20, 1033-1042.
34. Frazao, C., McVey, C.E., Amblar, M., Barbas, A., Vonrhein, C., Arraiano, C.M. and Carrondo, M.A. (2006) Unravelling the dynamics of RNA degradation by ribonuclease II and its RNA-bound complex. Nature, 443, 110-114.
35. Altman, S., Wesolowski, D., Guerrier-Takada, C. and Li, Y. (2005) RNase P cleaves transient structures in some riboswitches. Proc. Natl Acad. Sci. USA, 102, 11284-11289.
36. Jensen, K.G. (1993) The Escherichia coli K-12 "wild types" W3110 and MG1655 have an rph frameshift mutation that leads to pyrimidine starvation due to low pyrE expression levels. J. Bacteriol., 175, 3401-3407.